runs_manifest.csv file in the output directory instead of modifying samples.Rdata (#3708)tests/Rcheck_reference.log, which was used to ignore historic check messages that have now been fixed.Breaking: Ensemble runs now use shared input samples across all sites instead of independent sampling per site.
run.write.configs() now has two new required args ensemble.size and input_design, and removes ens.sample.method (#3535, #3612).runModule.run.write.configs() has new arg input_design, with default NULL meaning to generate one internally (#3535).create_execute_test_xml() and model_specific_tags(), which depended on deprecated database and web frontend (@S1DDHEY, #3826).settings$database$bety$write to FALSE (or undefining it entirely), at the obvious cost that runs set up this way are not recorded in the database (@yinghaoSunn, #3398).modellauncher in start_model_runs(),
including some support for array runs via settings like <qsub.extra>-t 1-@NJOBS@</qsub.extra>.start_model_runs and runModule_start_model_runs, both moved
from package PEcAn.remote (where they were start.model.runs and
runModule.start.model.runs). They kick off the model runs you set up
earlier in the workflow and handle the details of local or remote execution.